front 1 Selectional explaination | back 1 removal by natural selection |
front 2 Saturation explaination | back 2 many mutations on same site |
front 3 Models of evolution | back 3 allow to sample data to compensate for real life bias |
front 4 2 main variables of models of evolution | back 4 probability of mutations (costs of substitutions) frequency of bases |
front 5 Jukes-Cantor (JC) | back 5 equal frequency of bases all susbtitutions equal |
front 6 Kimura 2 parameter (K2P) | back 6 equal frequency of bases transitions not equal to transversions |
front 7 Felsenstein 1981 (F81) | back 7 different for each base all susbtitutions equal |
front 8 Hasegawa, Kishino, Yano (HKY48) | back 8 different for each base transitions not equal to transversions |
front 9 General Reversible (GTR) | back 9 different for each base different for each type of substitution |
front 10 Additional parameters | back 10 I: rate proportion of invariable sites G: gamma distributions: allows to show different mutation rates |
front 11 Assumptions | back 11 1. independence: mutations in one part of DNA, compensation mutation, Mutation in one site -> impact another. 2. Base composition: GC bias 3. variation in rates of substitution among sites |